Congruence, Consensus, and the Comparative Phylogeography of Codistributed Species in California

Lapointe, François‐Joseph; Rissler, Leslie J.

doi:10.1086/431283

Cited by 122 publications

(169 citation statements)

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“…Despite its extensive range, A. lugubris has not yet been the focus of a comprehensive phylogeographic study. Some phylogeographic data were collected for A. lugubris as part of a study of nine codistributed Californian species [35]. This previous study examined relationships between county level units of A. lugubris using an unrooted mtDNA tree, but the sampling was limited and it did not take into account the possibility of multiple genetic clades occupying the same county [35].…”

Section: Introductionmentioning

confidence: 99%

Cryptic diversity and biogeographical patterns within the black salamander (Aneides flavipunctatus) complex

Reilly

Wake

2014

Journal of Biogeography

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Aim Phylogeographical structure in the black salamander (Aneides flavipunctatus) was inferred using two independent genetic datasets. Concordance between the datasets was sought in order to evaluate earlier suggestions of species‐level breaks and evidence of vicariance and long‐term isolation within the complex. We hypothesized that major phylogeographical breaks would either correspond to current tectonic plate boundaries or to historical geological processes. Location North‐western California and southern Oregon (USA). Methods Three mitochondrial DNA (mtDNA) genes were sequenced for 240 black salamanders from 136 localities, and up to 13 nuclear DNA loci were sequenced for 145 black salamanders representing 93 localities. Phylogenetic analysis of our mitochondrial dataset was performed to recover major lineages, while spatial clustering analysis of our nuclear dataset was utilized to identify points of concordance with our mtDNA phylogeny. Levels of gene flow were estimated for all contact zones. Results Our mitochondrial phylogeny recovered four major lineages. Cluster analysis of our nuclear dataset is consistent with a four‐population scheme, with the boundaries matching those of the mtDNA lineages. Gene flow across a contact zone in southern Humboldt between two of the populational units is extremely limited (2Nm < 1). In what is identified as the Central Core population, two distinctive subpopulations were delineated based on nuclear data, but mitochondrial data are discordant. Main conclusions The Aneides flavipunctatus complex comprises at least four species‐level units. Two of the boundaries between these units are associated with current tectonic plate boundaries. The contact zone between our Northwest and Central Core populations lies adjacent to the Mendocino Triple Junction (MTJ), where the Humboldt and North American plates meet, while the area separating the Santa Cruz and Central Core populations corresponds to the boundary between the Pacific and Humboldt tectonic plates. The phylogeographical break within the Central Core population lies in a region in which uplift occurred that is associated with the historical position of the migrating MTJ.

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Section: Introductionmentioning

confidence: 99%

Cryptic diversity and biogeographical patterns within the black salamander (Aneides flavipunctatus) complex

Reilly

Wake

2014

Journal of Biogeography

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“…This region is noted for high levels of endemism in many taxa and is considered one of Earth's biodiversity hotspots (23,24). Studies of multiple taxa within the region have shown evidence of phylogeographic structure, much of which appears to coincide with boundaries established by past geologic events (25)(26)(27). The bryoflora of California is diverse and species-rich, including nearly 50% of the mosses documented for North America (2).…”

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confidence: 99%

Cryptic species within the cosmopolitan desiccation-tolerant moss Grimmia laevigata

Fernandez

Shevock

Glazer

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

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The common cushion moss Grimmia laevigata (Bridel) Bridel grows on bare rock in a broad range of environments on every continent except Antarctica. As such, it must harbor adaptations to a remarkably broad set of environmental stresses, the extremes of which can include very high temperatures, prolonged nearly complete desiccation, and high ultraviolet B (UVB) exposure. Yet, like many mosses, G. laevigata shows very little morphological variability across its cosmopolitan range. This presents an evolutionary puzzle, the solution to which lies in understanding the phylogeographic structure of this morphologically simple organism. Here we report the results of an analysis of amplified fragment length polymorphisms (AFLPs) in G. laevigata, focusing on individuals from the California Floristic Province. We found evidence that populations within California constitute two distinct geographically overlapping cryptic species. Each clade harbors multiple private alleles, indicating they have been genetically isolated for some time. We suggest that the existence of cryptic species within G. laevigata, in combination with its life history, growth habits, and extreme desiccation tolerance, makes this moss an ideal research tool and a candidate for a biological indicator of climate change and pollution.amplified fragment length polymorphisms ͉ bioindication ͉ California Floristic Province ͉ Grimmiaceae ͉ phylogeography

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“…Indeed, a search on "maximum agreement subtree" and "majority-rule tree" on Google Scholar 5 (http://scholar.google.com/) returned about 365 and 1140 results respectively. Among other things, MASTs are used as a metric to compare phylogenies [33,24,25], to compute the congruence index of phylogenetic trees [22,51], to identify horizontal gene transfer events [21], to resolve ambiguity in terraces in phylogenetic tree space [69], and as a consensus approach [14]. MRTs are used, among other things, to analyze phylogenetic trees from Bayesian analysis [43] and bootstrapping [27], two widely-used phylogenetic analysis techniques.…”

Section: Experiments On Biological Datamentioning

confidence: 99%

EvoMiner: frequent subtree mining in phylogenetic databases

et al. 2013

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The problem of mining collections of trees to identify common patterns, called frequent subtrees (FSTs), arises often when trying to interpret the results of phylogenetic analysis. FST mining generalizes the wellknown maximum agreement subtree problem. Here we present EvoMiner, a new algorithm for mining frequent subtrees in collections of phylogenetic trees. EvoMiner is an Apriori-like level-wise method, which uses a novel phylogeny-specific constant-time candidate generation scheme, an efficient fingerprinting-based technique for downward closure, and a lowest common ancestor based support counting step that requires neither costly subtree operations nor database traversal. Our algorithm achieves speed-ups of up to 100 times or more over Phylominer, the current state-of-the-art algorithm for mining phylogenetic trees. EvoMiner can also work in depth first enumeration mode, to use less memory at the expense of speed. We demonstrate the utility of FST mining as a way to extract meaningful phylogenetic information from collections of trees when compared to maximum agreement subtrees and majority rule trees ---two commonly used approaches in phylogenetic analysis for extracting consensus information from a collection of trees over a common leaf set. Disciplines Theory and AlgorithmsThis article is available at Iowa State University Digital Repository: http://lib.dr.iastate.edu/cs_techreports/11Noname manuscript No. The final publication is available at http://link.springer.com Abstract The problem of mining collections of trees to identify common patterns, called frequent subtrees (FSTs), arises often when trying to interpret the results of phylogenetic analysis. FST mining generalizes the well-known maximum agreement subtree problem. Here we present EvoMiner, a new algorithm for mining frequent subtrees in collections of phylogenetic trees. EvoMiner is an Apriori-like level-wise method, which uses a novel phylogeny-specific constant-time candidate generation scheme, an efficient fingerprinting-based technique for downward closure, and a lowest common ancestor based support counting step that requires neither costly subtree operations nor database traversal. Our algorithm achieves speed-ups of up to 100 times or more over Phylominer, the current state-of-the-art algorithm for mining phylogenetic trees. EvoMiner can also work in depth first enumeration mode, to use less memory at the expense of speed. We demonstrate the utility of FST mining as a way to extract meaningful phylogenetic information from collections of trees when compared to maximum agreement subtrees and majority rule trees -two commonly used approaches in phylogenetic analysis for extracting consensus information from a collection of trees over a common leaf set.

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Congruence, Consensus, and the Comparative Phylogeography of Codistributed Species in California

Cited by 122 publications

References 55 publications

Cryptic diversity and biogeographical patterns within the black salamander (Aneides flavipunctatus) complex

Cryptic diversity and biogeographical patterns within the black salamander (Aneides flavipunctatus) complex

Cryptic species within the cosmopolitan desiccation-tolerant moss Grimmia laevigata

EvoMiner: frequent subtree mining in phylogenetic databases

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